I'll continue on my little project later today Martin, regardless, you would always have heard from me
UPDATE: Hi Martin
I think there might be a slight misunderstanding (English is not my native language, as I'm Danish)

.
Initially, when I compiled, I didn't notice the progress percentage counting up (10%, 20%, etc.). I only focused on the end result showing an error message, so I assumed the compilation/flashing had failed completely because of lines like this at the end:
Running ninja in directory C:\FC_ESP_5.3\mtxesp32_s2_sdkconfig\build
Executing "ninja flash"...
Programming Failed.
C:\ProgramData\MatrixTSL\FlowcodeV11\FCD\ESP\Batch\esp32_prog.bat reported error code 0x1
Autoclose turned off
FINISHED
However, it turns out the ESP32-S2 actually gets programmed 100% fine and works perfectly! That is what confuses me—the program reaches the board successfully, but the console still reports "Programming Failed" at the very end.
I also just tried your suggestion of holding down the BOOT button, but it gave the exact same result: the error message still appears, even though the ESP is programmed correctly and runs as expected.
Thanks again for helping!
Best regards,
Jørgen